Interpretive Summary: The phenomenal advances in nucleic acid sequencing technologies have enabled many discoveries that might not have been made if it were not for this ability to efficiently sequence genomes and process massive amounts of data. Ironically, the technology that has made the concept of deep sequencing/metagenomics real, may present a challenge for scientists trying to design animal studies having the minimum of variables. In the not so distant past, the assumption that animals co-housed together were essentially the same was quite acceptable, especially in fields of study using outbred large animals. We study swine viral diseases and are continually vexed by the discovery of new viruses that challenge us as we try to produce a homogenous group of pigs for research. We report here the results of a small study using 4 pigs to evaluate the use of pyrosequencing technology as a potential screening method to determine the viruses that might be present in the pig, or its virome.

Technical Abstract:
The trial was successful in identifying a number of viruses in the feces of the pigs demonstrating the application of this technology to determine the background noise in the animals. The findings in this study are similar to the fecal virome in pigs from a typical commercial swine farm in the United States (Shan and others 2011). A variety of viruses were identified in pigs that were healthy or had diarrhea. There were more RNA viruses than DNA viruses detected. The spectrum of viruses observed included Astroviridae, Caliciviridae, Coronaviridae, Arteriviridae, Picornaviridae, Picobinavirida and Parvoviridae. In the previous study, Kobuviruses were identified at a rate 12 times higher in healthy pigs than in sick pigs. In the present study, Sapovirus was identified at a remarkably high frequency in the two healthy pigs and barely at all in the pig infected with PRRSV or in the pig that had chronic diarrhea. Such differences are not clear at the present time. This technology can provide a more complete picture of the viruses co-existing in the experimental animal and insight into strategies that may improve the production of pork.